text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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# -*- coding: utf-8 -*-
# Copyright (C) 2017 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc., University of Heidelberg, and University of
# of Connecticut School of Medicine.
# All rights reserved.
# Copyright (C) 2010 - 2016 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc., Universit... | jonasfoe/COPASI | copasi/bindings/python/unittests/Test_CreateSimpleModel.py | Python | artistic-2.0 | 7,093 | [
"COPASI"
] | 579ab4c7c4d6959ad4a3cd6728bba1a8d5bff88cf2067033194d90bddbdbce18 |
# pylint: disable=arguments-differ
""" Models for the shopping cart and assorted purchase types """
from collections import namedtuple
from datetime import datetime
from datetime import timedelta
from decimal import Decimal
import json
import analytics
from io import BytesIO
from django.db.models import Q, F
import py... | naresh21/synergetics-edx-platform | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 91,630 | [
"VisIt"
] | 0627c6b9e2084f1168ba1d07f1568701bcd1a32bb85d636dbbdd0d9b6eb866d5 |
# Copyright 2002 by Andrew Dalke. All rights reserved.
# Revisions 2007-2008 by Peter Cock.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
# Note that BioSQL (including the database schema and scr... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/BioSQL/__init__.py | Python | gpl-2.0 | 556 | [
"Biopython"
] | 34455b919babee3abd3d2e6637946af384783789a17a402c874bc79efed22b24 |
#!/usr/bin/env python
# =========================================================================
#
# Copyright NumFOCUS
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http:/... | richardbeare/SimpleITK | Examples/DemonsRegistration2/DemonsRegistration2.py | Python | apache-2.0 | 3,096 | [
"Gaussian"
] | 9b0f69ec4cafe53623c6bf1ee50783bc8096ae466dcbcd0a13f7f039e1c6c56d |
import os
import re
import json
import random
import tempfile
from django import forms
from django.urls import reverse
from django.http import HttpResponse, JsonResponse
from django.views.generic.base import View
from django.views.decorators.http import require_http_methods
from django.shortcuts import get_object_or_4... | ginkgobioworks/edge | src/edge/views.py | Python | mit | 28,250 | [
"BLAST"
] | d413ebb026ebbbce899bd77a5efda93413e3e7d4abed6089564d300513dfcaa1 |
# Copyright (C) 2012 Olaf Lenz
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ESPR... | roehm/espresso | testsuite/configs/check_myconfig_complete.py | Python | gpl-3.0 | 1,587 | [
"ESPResSo"
] | 179d24653a7d5df1e8f9859ecb5301992a6c26f194c34bcfc1264e37b1307c08 |
import logging
import numpy as np
import os.path
from ast import literal_eval
from warnings import warn
import nibabel as nib
from dipy.core.gradients import gradient_table
from dipy.data import default_sphere
from dipy.io.gradients import read_bvals_bvecs
from dipy.io.peaks import save_peaks, peaks_to_niftis
from d... | FrancoisRheaultUS/dipy | dipy/workflows/reconst.py | Python | bsd-3-clause | 44,675 | [
"Gaussian"
] | 4b1da6556daec8657afecbac40f1bda50fcb901d88625aa786ec58d1ef918175 |
#!/usr/bin/env python
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2011, 2012 Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU G... | zenoss/ZenPacks.zenoss.CloudStack | ZenPacks/zenoss/CloudStack/poll_cloudstack.py | Python | gpl-2.0 | 21,076 | [
"VisIt"
] | 0b7da490713f1d787a4c0b015150e235fc430fc8b763a5366edcb75ae617e9dc |
################################################################################
# Peach - Computational Intelligence for Python
# Jose Alexandre Nalon
#
# This file: tutorial/linear-prediction.py
# Using neural networks to predict number sequences
#######################################################################... | anki1909/peach | tutorial/neural-networks/linear-prediction.py | Python | lgpl-2.1 | 3,386 | [
"Gaussian",
"NEURON"
] | 3830e6442f013865de2d8d091db70b82462e0af684c3470c9c895f9b4dfde59f |
"""
Summarize hits in a blast file based on the sequences present
"""
import os
import sys
import argparse
from roblib import stream_fasta, stream_blast_results
def seq_lengths(fafile, verbose=False):
"""
Read the sequence length from a fasta file
:param fafile: the fasta file to read
:param verbose: ... | linsalrob/EdwardsLab | blast/summarize_blast.py | Python | mit | 1,172 | [
"BLAST"
] | 7031cd0e1a25fb01d4b8dc04551e2fc54f5395c84702c2f33a610a5a14ebecb7 |
# $Id$
#
# Copyright (C) 2002-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" Atom-based calculat... | rvianello/rdkit | rdkit/Chem/Crippen.py | Python | bsd-3-clause | 6,149 | [
"RDKit"
] | 81476be8f99d3f2a231fd9d182b74e48ee16eb82ca0d96151d02d981c4c24f26 |
"""
LAMMPS EEX I/O
"""
import pandas as pd
import math
import numpy as np
import eex
from . import lammps_metadata as lmd
import logging
logger = logging.getLogger(__name__)
def write_lammps_file(dl, data_filename, input_filename, unit_style="real", blocksize=110):
# handle units
unit_set = lmd.units_styl... | dgasmith/EEX_scratch | eex/translators/lammps/lammps_write.py | Python | bsd-3-clause | 5,929 | [
"LAMMPS"
] | e1fa0032ded843bf2c3e9eeb17b0cbc63c8518cc9d95716cb44ba8b014cf4b9d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
""" Initialize the component for the CNMF
contain a list of functions to initialize the neurons and the corresponding traces with
different set of methods like ICA PCA, greedy roi
"""
#\package Caiman/source_extraction/cnmf/
#\version 1.0
#\copyright GNU General Publi... | agiovann/Constrained_NMF | caiman/source_extraction/cnmf/initialization.py | Python | gpl-2.0 | 83,794 | [
"Gaussian",
"NEURON"
] | 865005a7aee890a50c124be55a9fcf26ddeaafc8c6e80efc213e462dd8b68f91 |
#!/usr/bin/env python3
import logging
import logging.config
import sys
logging.config.fileConfig('../logging.conf')
log = logging.getLogger('memory')
class Memory(object):
"""GameBoy Memory
==============
Memory Map
==========
Start End Description
----- --- -----------
... | jonwells90/PyBoy | PyBoy/memory.py | Python | mit | 2,287 | [
"FEFF"
] | 0fd96477a0296425af68940ce823b8bd4c01f5de10a17eed2a9780e33ce1d6a8 |
"""
Various splitters
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from rdkit import Chem
from rdkit.Chem.Scaffolds import MurckoScaffold
from tqdm import tqdm
def generate_scaffold(smiles, include_chirality=False):
"""
Compute the Bemis-Murcko scaffold for a SMILES string.
Not... | DentonJC/virtual_screening | moloi/splits/scaffold_split.py | Python | gpl-3.0 | 2,394 | [
"RDKit"
] | 71d7a79065d6ef82c2bcab474c3f1d84c2ae858b4f99f72226fab9a1dc577ad4 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Apr 17 12:41:17 2017
@author: kostenko
Simulate makes fake polychromatic x-ray CT data
"""
#import tomopy.misc
#import tomobox as tw
#import xraydb
class spectra():
'''
Simulates spectral phenomena that involve x-ray-matter interaction
'... | cicwi/tomo_box | simulate.py | Python | gpl-3.0 | 4,567 | [
"Gaussian"
] | fad39c62dd0b7b1f8f8e38e94a61a289c21d53a92d47964dc1be0aa28884262b |
"""Core implementation of the testing process: init, session, runtest loop."""
import argparse
import fnmatch
import functools
import importlib
import os
import sys
from typing import Callable
from typing import Dict
from typing import FrozenSet
from typing import Iterator
from typing import List
from typing import Opt... | KiChjang/servo | tests/wpt/web-platform-tests/tools/third_party/pytest/src/_pytest/main.py | Python | mpl-2.0 | 31,889 | [
"VisIt"
] | 72a2cc30f717b3756ea56607242872b96a6966a2d8bf4d36085b4bf85cc633c0 |
# Copyright 2021 DeepMind Technologies Limited. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | deepmind/mctx | mctx/_src/tests/policies_test.py | Python | apache-2.0 | 10,164 | [
"VisIt"
] | 00e374c21eefac51ba24f7337e55fce645313d0491a007ec99b6a6f6e13d3705 |
"""
Functions to operate on polynomials.
"""
from __future__ import division, absolute_import, print_function
__all__ = ['poly', 'roots', 'polyint', 'polyder', 'polyadd',
'polysub', 'polymul', 'polydiv', 'polyval', 'poly1d',
'polyfit', 'RankWarning']
import functools
import re
import warnings
i... | gfyoung/numpy | numpy/lib/polynomial.py | Python | bsd-3-clause | 39,818 | [
"Gaussian"
] | 2061e8c513a396358c432d05a21e0c7b1fba2022ecd24f99a2462f7aa78d5d6b |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | wizmer/NeuroM | neurom/__init__.py | Python | bsd-3-clause | 3,437 | [
"NEURON"
] | 365899993a355a5be42424f4a95fb8937415c3d516fa9dabdec4eb798b813824 |
"""Test for memory leaks in the CNA code."""
import asap3
from ase.lattice.compounds import L1_2
import numpy as np
steps = 30
msteps = 5
def makeatoms():
atoms = L1_2(size=(10,10,10), symbol=('Au', 'Cu'), latticeconstant=4.0)
r = atoms.get_positions()
r += np.random.normal(0.0, 0.0001, r.shape)
atom... | auag92/n2dm | Asap-3.8.4/Test/CNAleak.py | Python | mit | 1,950 | [
"ASE"
] | 75060680bfe5793d20a116888cf709b4e72735749e8e37f1f350e266f202087a |
"""Neural machine translation example.
This is a pretty straightforward implementation of Badhanau et al. (2014):
https://arxiv.org/pdf/1409.0473v7.pdf
The system is word based and assumes tokenized inputs, the only bells and
whistles are variational dropout and layer normalization. Otherwise this is
meant as a start... | robertostling/bnas | examples/nmt.py | Python | gpl-3.0 | 10,029 | [
"Gaussian"
] | 061bdccd094bb9fa1edb1b115712c8e369ab8562cdcf00e31260db19656d75d3 |
#!/usr/bin/env python
import pysam
import argparse
import matplotlib.pyplot as plt
import numpy as np
ap = argparse.ArgumentParser(description="Print the nucleotide frequency of a pileup.")
ap.add_argument("--bam", help="Input bam file.", required=True)
ap.add_argument("--freq", help="Print the frequency to this file... | yunlongliukm/chm1_scripts | PrintFrequency.py | Python | mit | 1,551 | [
"pysam"
] | bad33329e56ce513297cb658f9e15baff45694a691849f35bea0a154fcb6e1c2 |
from builtins import str
from builtins import range
from builtins import object
import logging
import datetime
import time
import os
import shutil
import tempfile
import re
import traceback
import json
import hashlib
from biomaj_core.utils import Utils
from biomaj_download.downloadclient import DownloadClient
from bio... | horkko/biomaj | biomaj/workflow.py | Python | agpl-3.0 | 74,620 | [
"BLAST"
] | 1b98349be440a53b3febc210cb8389ce26833daffc938ae67aed05f5d3acc5db |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class AtomDft(MakefilePackage):
"""ATOM is a program for DFT calculations in atoms and pseudopot... | LLNL/spack | var/spack/repos/builtin/packages/atom-dft/package.py | Python | lgpl-2.1 | 1,050 | [
"SIESTA"
] | d243299ef29308f4c4cf317bc8acff65e9e843068b6a0c7aa8f396868bb15b9d |
import logging
import king_phisher.plugins as plugin_opts
import king_phisher.server.database.manager as db_manager
import king_phisher.server.database.models as db_models
import king_phisher.server.plugins as plugins
import king_phisher.server.signals as signals
import smoke_zephyr.utilities as utilities
try:
impo... | securestate/king-phisher-plugins | server/xmpp_notifications.py | Python | bsd-3-clause | 5,126 | [
"VisIt"
] | bed2d2924a03b6eabeb388f23fe2aca534bdb7afa2143968f44d1224e83b51b6 |
# -*- coding: utf-8 -*-
"""
.. _tut-artifact-ica:
Repairing artifacts with ICA
============================
This tutorial covers the basics of independent components analysis (ICA) and
shows how ICA can be used for artifact repair; an extended example illustrates
repair of ocular and heartbeat artifacts.
We begin as... | kambysese/mne-python | tutorials/preprocessing/plot_40_artifact_correction_ica.py | Python | bsd-3-clause | 31,514 | [
"Gaussian"
] | 75b7d90a386f2a89971796dee2662494cea8b8c44efba77697b99cfdd00d38f8 |
from views import *
from lookups import *
import requests
import re
from utils import *
import itertools
from config import config
if config.IMPORT_PYSAM_PRIMER3:
import pysam
import csv
#hpo lookup
import orm
def individuals_update(external_ids):
patients_db=get_db(app.config['DB_NAME_PATIENTS'])
users_d... | Withington/phenopolis | views/my_patients.py | Python | mit | 6,095 | [
"pysam"
] | a1f3ed17f6c52decdd7e41ec46a0fc7ae8027637849a144bd2cdddd09fb494f4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Example script loading and execiting a simulation with the
Hay et al. 2011 L5b-pyramidal cell model, which is implemented by default
using templates.
This script assume that the model files is downloaded and unzipped inside
this folder from ModelDB:
http://senselab.med... | LFPy/LFPy | examples/example_loadL5bPCmodelsEH.py | Python | gpl-3.0 | 3,737 | [
"NEURON"
] | 0183169ce60210a3ca6eea311b0b9d7d0e494ea808eed5b1822893c4838a19ad |
import os
import numpy as np
from functools import partial
from menpo.base import name_of_callable
from menpo.shape import bounding_box
from menpofit.visualize import print_progress
from menpo.visualize import print_dynamic
from menpo.transform import Scale
from menpo.image import Image
from .correlationfilter import... | nontas/trafficsignrecognition | trafficsignrecognition/base.py | Python | bsd-3-clause | 32,400 | [
"Gaussian"
] | 91cfc4adf5cdc7f672c62ed7b8a7cc06c488ec40c53ff0de65ac297f06c3f564 |
# -*- coding: utf-8 -*-
"""
mchem.fps
~~~~~~~~~
Functions for generating fingerprints using RDKit.
:copyright: Copyright 2014 by Matt Swain.
:license: MIT, see LICENSE file for more details.
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
from collect... | mcs07/mongodb-chemistry | mchem/fps.py | Python | mit | 4,263 | [
"RDKit"
] | 6c3e5055ec983fce452ac3b6c4c6457a46ab8dd2b7b31e6d82a00a97c2c3d10a |
# coding: utf-8
from __future__ import unicode_literals, division
import glob
import logging
import shlex
import socket
import re
import time
from pkg_resources import parse_version
"""
This module implements basic kinds of jobs for QChem runs.
"""
import os
import shutil
import copy
import subprocess
from pymatgen... | davidwaroquiers/custodian | custodian/qchem/jobs.py | Python | mit | 23,412 | [
"pymatgen"
] | 34bce716bc14af4c5f2a528a22a682a3c9a688a53938db5676d0548cf988cdd8 |
try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
InterpolateDataSetAttributes()
| jeromevelut/Peavip | Testing/InterpolateDataSetAttributes.py | Python | gpl-3.0 | 141 | [
"ParaView"
] | d6ffcb956b6034d732319938c1841d84b39ed92c13063649a6086219ada4d904 |
#!/usr/bin/env python
#file decontaminate.py: helper functions for removing contaminants
__author__ = "Jon Sanders"
__copyright__ = "Copyright 2014, Jon Sanders"
__credits__ = ["Jon Sanders"]
__license__ = "GPL"
__version__ = "1.9.1"
__maintainer__ = "Jon Sanders"
__email__ = "jonsan@gmail.com"
from biom import load_... | tanaes/decontaminate | qiime_scripts/qiime/decontaminate.py | Python | mit | 16,496 | [
"BLAST"
] | 0de04c6905071b5eac25d49fad8f0a400e500cd9358bfe23579757c57b1808a7 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This class implements smart io classes that performs intelligent io based on
file extensions.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright... | Bismarrck/pymatgen | pymatgen/io/smart.py | Python | mit | 6,754 | [
"Gaussian",
"VASP",
"pymatgen"
] | 8b9a4c33b8177da78432925024cbe8e45f753325fc08b056ea8826d12cc31b1f |
import unittest
import json
from freezegun import freeze_time
from datetime import datetime, timedelta
from eachday.tests.base import BaseTestCase
from eachday.models import User, BlacklistToken
from eachday import db
class TestAuthRoutes(BaseTestCase):
def test_registration(self):
''' Test for user regi... | bcongdon/EachDay | eachday/tests/test_auth.py | Python | mit | 9,773 | [
"MOE"
] | 1be1db7586884d2048bc6407106223a2f9becec1f16800a77bb1169528a22d7c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import warnings
"""
Created on Mar 19, 2012
"""
__author__ = "Shyue Ping Ong, Stephen Dacek"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__em... | richardtran415/pymatgen | pymatgen/entries/tests/test_compatibility.py | Python | mit | 80,319 | [
"pymatgen"
] | 9b02910a6873324c3d4a0deee56172bd9c01a43a31c9e04261b40fec47db47b7 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | le9i0nx/ansible | lib/ansible/modules/network/avi/avi_cloudconnectoruser.py | Python | gpl-3.0 | 4,708 | [
"VisIt"
] | e629b2a9203397e58dabc7aef1e12da4eca703ec7f2328b037d6fe85a03bf808 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | mkuron/espresso | src/python/espressomd/comfixed.py | Python | gpl-3.0 | 1,349 | [
"ESPResSo"
] | 151580e9836fa5ea971211572c68d6e8a7681dc50304ac9563e7856b4d3bdc6c |
"""
Single page performance tests for Studio.
"""
from bok_choy.web_app_test import with_cache
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.studio.overview import CourseOutlinePage
from ..tests.helpers import AcceptanceTest
class StudioPagePerformanceTest(... | ahmedaljazzar/edx-platform | common/test/acceptance/performance/test_studio_performance.py | Python | agpl-3.0 | 3,348 | [
"VisIt"
] | 8cbcfffe21f6a998f120428c9fc29064b96392235370b112a08bfef1f5a5433c |
"""
==========================
DKI MultiTensor Simulation
==========================
In this example we show how to simulate the diffusion kurtosis imaging (DKI)
data of a single voxel. DKI captures information about the non-Gaussian
properties of water diffusion which is a consequence of the existence of tissue
barri... | sinkpoint/dipy | doc/examples/simulate_dki.py | Python | bsd-3-clause | 5,070 | [
"Gaussian"
] | 2bb1bd50b22a9287ef34bfbad13e7ae665238513c5d561cc42e8712275667147 |
"""
SCATTER_ADVANCED.PY
Support material for the blog post "Working with Spyder", on Programando
Ciência.
* Author: Alexandre 'Jaguar' Fioravante de Siqueira
* Contact: http://www.programandociencia.com/about/
* Support material:
http://www.github.com/alexandrejaguar/programandociencia
* In order to cite this ma... | alexandrejaguar/programandociencia | 2016/0508-scatteradv/scatter_advanced.py | Python | gpl-2.0 | 5,408 | [
"Jaguar"
] | e543e891d47f0d21c98b3795175eeb56b02f39f613eac5dd1c88cdb8f9fb3b93 |
# -*- coding: utf-8 -*-
#
# documentation build configuration file, created by
# sphinx-quickstart on Wed Mar 2 11:37:36 2016.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All confi... | janmedlock/HIV-95-vaccine | docs/conf.py | Python | agpl-3.0 | 10,557 | [
"Amber"
] | 406dad324cc57471ad3a6bf120cd1099092b8ad6ee7c8353ebb3a3ec865ef673 |
# -*- coding: utf-8 -*-
from Visitor.CNodeVisitor import *
from CNode import *
from helper.id import identity
from helper.timeconv import *
from helper.icalconv import *
from helper.recurrence import *
from hashlib import sha1
import datetime
class ToLowerCaseVisitor(CNodeVisitor):
def visit_any(self, o):
... | orbekk/erebus | Visitor/ICS2ErebusVisitor.py | Python | gpl-2.0 | 4,075 | [
"VisIt"
] | b7866f1392b32989c35d1094bf6fd616cbef787330b378a55804f4eea1571314 |
"""
Functions for automatic selection optimisation.
"""
import warnings
import numpy as np
import matplotlib.pyplot as plt
from scipy.stats import bayes_mvs
from scipy.stats.kde import gaussian_kde
from latools.helpers import Bunch, _warning
from latools.helpers.signal import rolling_window, bool_2_indices
from latools... | oscarbranson/latools | latools/filtering/signal_optimiser.py | Python | mit | 19,522 | [
"Gaussian"
] | 782b64a273afebcc1951c949aa6a9bf915c8f7de892f18c12e6c7d8c6209325c |
"""sim_utils.py:
Helper function related with simulation.
Last modified: Sat Jan 18, 2014 05:01PM
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
__credits__ = ["NCBS Bangalore", "Bhalla Lab"]
__license__ = "GPL"
__version__ = ... | subhacom/moose-core | python/moose/sim_utils.py | Python | gpl-3.0 | 2,098 | [
"MOOSE"
] | 5de8e1ea30ee8f93f5cf8657db274786a6f4680a8aeb93f9d56c673dff3b83f5 |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.moltemplate.org
# http://www.chem.ucsb.edu/~sheagroup
# License: MIT License (See LICENSE.md)
# Copyright (c) 2013, Regents of the University of California
# All rights reserved.
"""
lttree.py
lttree.py is an extension... | smsaladi/moltemplate | moltemplate/lttree.py | Python | bsd-3-clause | 46,054 | [
"LAMMPS"
] | 02a35d4d6022865243ca022dea85138f064a1e8b18614954a888500b69477591 |
__author__ = 'civa'
OBJECT_TYPES = dict(STAR=0, CATALOG_STAR=1, PLANET=2, OPEN_CLUSTER=3, GLOBULAR_CLUSTER=4,
GASEOUS_NEBULA=5, PLANETARY_NEBULA=6, SUPERNOVA_REMNANT=7, GALAXY=8,
COMET=9, ASTEROID=10, CONSTELLATION=11, MOON=12, ASTERISM=13,
GALAXY_CLUSTER=14, DARK_NEBULA=15, QUASAR=16, MULT_STAR=17, RADIO_SOURCE=18... | Civa/Zenith | src/Backend/Distributed/shared/tables.py | Python | gpl-3.0 | 1,723 | [
"Galaxy"
] | 24d1364b609b63120e61ee7e20d4a890d21dc9cb759a1f73e27dcaa418b3989b |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/controls/delegates/plaintextdelegate.py | Python | gpl-2.0 | 2,645 | [
"VisIt"
] | 58595ba2296358f754948df5f4e6f9e84a855fce488f2dfe94127b7dcd465c91 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/io/format/tests/test_newick.py | Python | bsd-3-clause | 12,594 | [
"scikit-bio"
] | 7c9bcafa96b229e5b563be25286390b0e6f67b3b84c817257590fc745dc44bc2 |
'''
Functions for working with DESI mocks and fiberassignment
TODO (maybe):
This contains hardcoded hacks, especially wrt priorities and
interpretation of object types
'''
from __future__ import print_function, division
import sys, os
import numpy as np
from astropy.table import Table, Column
from fiberassign import... | desihub/fiberassign | old/py/mock.py | Python | bsd-3-clause | 3,161 | [
"Galaxy"
] | 1cb4cca42a55d8140ae3eb9ab3186980f652b8985d4c59aa7958d37b2a6a5a2b |
## -*- coding: utf-8 -*-
## Copyright (c) 2015-2020, Exa Analytics Development Team
## Distributed under the terms of the Apache License 2.0
#"""
#Parser for ADF Output
##########################
#Parser for the output of the DIRAC program (part of the ADF suite).
#"""
#import pandas as pd
#from exa import Parser, Matc... | exa-analytics/atomic | exatomic/adf/adf/adf.py | Python | apache-2.0 | 1,460 | [
"ADF",
"DIRAC"
] | b15c7c1e15bbfbb8cc01dc3f4f8ac463bae3e18483fd98d7bb0db1d75841906a |
#!/usr/bin/env python3
# [1] https://doi.org/10.1063/1.1515483 optimization review
# [2] https://doi.org/10.1063/1.471864 delocalized internal coordinates
# [3] https://doi.org/10.1016/0009-2614(95)00646-L lindh model hessian
# [4] 10.1002/(SICI)1096-987X(19990730)20:10<1067::AID-JCC9>3.0.CO;2-V
# Handling of corn... | eljost/pysisyphus | deprecated/intcoords/InternalCoordinatesOld.py | Python | gpl-3.0 | 29,577 | [
"Gaussian"
] | 63fdb965159c68d5f5e7ccde73d56110cd5bcee015424a9a88cdca2370c1faf9 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | primoz-k/parilis | config/urls.py | Python | bsd-3-clause | 1,229 | [
"VisIt"
] | 5a078ee8a3b36ff80fef8c88cfb67e6feb0575b0ea734d5444854a5dbfeea7cc |
from __future__ import annotations
import collections
import itertools
import math
import types
import wx
from wx.lib.intctrl import IntCtrl
from cctbx import crystal, uctbx
from cctbx.miller import index_generator
from dxtbx.imageset import ImageSet
from dxtbx.model.detector_helpers import get_detector_projection_2... | dials/dials | util/image_viewer/spotfinder_frame.py | Python | bsd-3-clause | 116,312 | [
"CRYSTAL"
] | 3ab9850899fec2857fe31cb86e2157ebd65afc5954edef25244cb2957e84fddc |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Gregory Bowman
# Contributors: Robert McGibbon
#
# MDTraj is f... | rmcgibbo/mdtraj | tests/test_io.py | Python | lgpl-2.1 | 4,978 | [
"MDTraj"
] | 69e8cf7f4f9ca135bfe9c387fd76ff81577729726398ab37b827e5cebf77f2a8 |
"""
Support code for the freedesktop.org basedir spec.
This module provides functions for locating configuration files.
@see: U{http://freedesktop.org/wiki/Standards/basedir-spec}
@var home: The value of $HOME (or '/' if not set). If we're running as root and
$HOME isn't owned by root, then this will be root's home ... | pombredanne/zero-install | zeroinstall/support/basedir.py | Python | lgpl-2.1 | 5,004 | [
"VisIt"
] | 99329136c3457280c598edf5f483b39bfff25d869333d95415ea6994f5173516 |
import pytest
from lissero.scripts.Blast import Blast
run_blast = Blast()
def test_blast_version(blast_version):
run_blast.version()
expected = tuple(blast_version.split("."))
assert expected == run_blast.version_no
| MDU-PHL/LisSero | tests/test_BlastClass.py | Python | gpl-2.0 | 232 | [
"BLAST"
] | e3b43526332753d2f349640623b05200978a574a37f9e1deb9310b5cc94357d1 |
"""
Python Interchangeable Virtual Instrument Library
Copyright (c) 2012-2017 Alex Forencich
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the... | python-ivi/python-ivi | ivi/agilent/agilent3000A.py | Python | mit | 6,792 | [
"Gaussian"
] | 7f8099e2822c33603176c3d271b1ae79002c3a345df5a9c39d6211a186af1084 |
# -*- coding: utf-8 -*-
# SyConn - Synaptic connectivity inference toolkit
#
# Copyright (c) 2016 - now
# Max Planck Institute of Neurobiology, Martinsried, Germany
# Authors: Philipp Schubert
import datetime
import glob
import logging
import os
from logging import Logger
from typing import Tuple, Optional, Union, Dict... | StructuralNeurobiologyLab/SyConn | syconn/handler/config.py | Python | gpl-2.0 | 34,923 | [
"NEURON"
] | 5c541c00d94fb4b8392ed47121b43775ed45c4cff97c414ddf60f7c8b2500335 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2006-2010 Edgewall Software
# All rights reserved.
#
# This software is licensed as described in the file COPYING, which
# you should have received as part of this distribution. The terms
# are also available at http://genshi.edgewall.org/wiki/License.
#
# This software consist... | Lyleo/OmniMarkupPreviewer | OmniMarkupLib/Renderers/libs/python3/genshi/template/eval.py | Python | mit | 21,040 | [
"VisIt"
] | 538bb7c1e4460ffd237ee4969124e5e340a2ccf4b3d0d1b6689e068cd252bf08 |
"""A simple example of how to use IPython.config.application.Application.
This should serve as a simple example that shows how the IPython config
system works. The main classes are:
* IPython.config.configurable.Configurable
* IPython.config.configurable.SingletonConfigurable
* IPython.config.loader.Config
* IPython.... | pioneers/topgear | ipython-in-depth/examples/Customization/appconfig.py | Python | apache-2.0 | 3,290 | [
"Brian"
] | 12734d94645cb21d94adf0f7b65c94958336b4b496bb5d336ca76a7fb6c2ffb4 |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.uk/wiki... | acsis-project/emissions | emissions/python/periodic_1960/regrid_C3H8_emissions_n96e_360d_1960.py | Python | gpl-3.0 | 7,136 | [
"NetCDF"
] | 39632054268ee6dc0dea91fef40e078d7416f732180456e60d36ef4e317305fd |
from UTILS import *
from UTILS.BED import maskChr,mask,BED
from VCF import gz,VCF
def loadPiarPop(f,pop,popxp,negate=False):
load=pd.read_pickle
if f[-3:]=='.gz':load=gz.load
try:return load(f.format(pop, popxp))
except:
alpha=(1,-1)[negate]
return load(f.format(popxp, pop))*alpha
clas... | airanmehr/Utils | Genome.py | Python | mit | 12,815 | [
"Bioconda",
"pysam"
] | 3859aabe755e12cb76f4798ca10a73614960e7831a77ac83df41bab736986418 |
# Docstrings for generated ufuncs
#
# The syntax is designed to look like the function add_newdoc is being
# called from numpy.lib, but in this file add_newdoc puts the
# docstrings in a dictionary. This dictionary is used in
# _generate_pyx.py to generate the docstrings for the ufuncs in
# scipy.special at the C level... | tylerjereddy/scipy | scipy/special/_add_newdocs.py | Python | bsd-3-clause | 258,381 | [
"Gaussian"
] | ec39b5cad61b108c247317ab1128a71c02d08fe3110665dc02ef715dbe7fef91 |
import vtk
import matplotlib.cm as cm
import sys
LABEL_NAMES = [\
'olfactory bulb',
'cerebral cortex',
'lateral septal nuclei',
'striatum',
'globus pallidus',
'thalamus',
'hypothalamus',
'hippocampal formation',
'superior colliculus',
'inferior colliculus',
'cerebellum',
'fimbria',
'internal capsule',
'ventricle',
've... | neuroinformatics/bah2015_registration | vtk_test/interactive_intensity.py | Python | mit | 5,692 | [
"VTK"
] | 35b9c923028a54deed3686bd93b226b42b0ff88c72fd64dedb52371dd6e3dad8 |
"""Integration test using a simple dummy model definition."""
# Copyright 2016 Andrew Dawson
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
#... | aopp-pred/scmtiles | scmtiles/test/integration/test_simple.py | Python | apache-2.0 | 7,178 | [
"NetCDF"
] | 9c536f194956b2a611205a8cf6a74fcb26b67ab54f5127f914ba1ea874c2b551 |
""" AlwaysDegradedPolicy module
"""
from DIRAC import S_OK
from DIRAC.ResourceStatusSystem.PolicySystem.PolicyBase import PolicyBase
class AlwaysDegradedPolicy(PolicyBase):
"""
The AlwaysDegradedPolicy is a dummy module that can be used as example, it
always returns Degraded status.
"""
@staticme... | ic-hep/DIRAC | src/DIRAC/ResourceStatusSystem/Policy/AlwaysDegradedPolicy.py | Python | gpl-3.0 | 606 | [
"DIRAC"
] | f47bdddd6117cf2d020a5ffa8c6089be671dc62b940df6193f1d588d95a6f288 |
import os
import time
import yaml
import json
import datetime
import numpy as np
import pandas as pd
from time import strftime
from pprint import pprint
import matplotlib.pyplot as plt
from diffpy.Structure import loadStructure
from diffpy.Structure import StructureFormatError
from diffpy.srreal.structureadapter impor... | chiahaoliu/pdf_lib | pdf_lib/calculate.py | Python | mit | 13,026 | [
"pymatgen"
] | 8dd8e8ea8d711f6999ee21b0a515958e7cfd0dde906721607995339e765aa71d |
#!/usr/bin/python
# coding=utf-8
from wikitools import wiki, wikifile
""" Because the Veekun sprite rips of gen1/2 are non-transparent, they must be downloaded from Bulbapedia instead """
def main():
site = wiki.Wiki("http://bulbapedia.bulbagarden.net/w/api.php")
img_root = "/var/projects/namerater/assets/pok... | DrDos0016/namerater | tools/download_gen1-2.py | Python | mit | 3,435 | [
"CRYSTAL"
] | 6a271f4b8adaa34fa245897935d9ba114e6ad9034689fa9d05a6078c1b4e92a8 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import time
# !! This is the configuration of Nikola. !! #
# !! You should edit it to your liking. !! #
# ! Some settings can be different in different languages.
# ! A comment stating (translatable) is used to denote those.
# ! There are two ways to ... | bjwnjm/bjwnjm.github.io | conf.py | Python | apache-2.0 | 53,455 | [
"VisIt"
] | d03c526671fb3c522c4502bdf56b61ea3b822242ce7ad505055186feb584e092 |
# !usr/bin/env python2
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2017-02-12 20:46:42
# @Last modified by: Brian Cherinka
# @Last Modified time: 2017-02-22 10:40:26
from __future__ import print_function, division, absolute_import
from marvin.tests.web im... | bretthandrews/marvin | python/marvin/tests/web/test_index.py | Python | bsd-3-clause | 5,525 | [
"Brian",
"Galaxy"
] | fc42bac1b8eb73d30310bc67cf17ebec07144be9fcb75176a2b61ec468cae188 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | swails/mdtraj | mdtraj/__init__.py | Python | lgpl-2.1 | 3,351 | [
"Amber",
"CHARMM",
"Gromacs",
"MDTraj",
"NAMD",
"NetCDF"
] | 4422f12207c7984c99a934941666bd739d121a4a26ab29d2931be4a537e902ea |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
All the pure-Python 'helper' functions which were previously included in the
Pyke rules database 'fc_rules_cf.krb'.
The 'a... | SciTools/iris | lib/iris/fileformats/_nc_load_rules/helpers.py | Python | lgpl-3.0 | 42,793 | [
"NetCDF"
] | 992be2f10c33fc9e8c786824be416e95bff78ab7cebfd0727f0470094061cd8a |
from numpy import *
from refractive_index import *
# function to computer soil dielectric constant using Mironov et al 2009
# Brian Hornbuckle, May 25, 2010.
# Converted to Python by Jason Patton, January 10, 2012
# uses function "refractive_index.m"
# output: n = n' - j*n" = moist soil index of refraction, ejwt tim... | jasoncpatton/TbSim | n_soil.py | Python | mit | 3,176 | [
"Brian"
] | 1f0dca5855ac9730b9df8d0f78760e912b0fc91b014c6821456e22c427e09f7f |
#!/usr/bin/env python
# B a r a K u d a
#
# Budget and other stuffs on rectangular boxes!
#
# L. Brodeau, 2013
import sys
import numpy as nmp
from netCDF4 import Dataset
from os.path import basename
import barakuda_tool as bt
import barakuda_ncio as bnc
from barakuda_physics import sigma0
#next = 1... | plesager/barakuda | python/exec/budget_rectangle_box.py | Python | gpl-2.0 | 14,348 | [
"ORCA"
] | 058ca02d70663da4562acdc0238d4a2bc8988fa7d3ee16e825e9d56ee70d3156 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
# A list of all valid configuration keywords for a measurement.
# The variable names depict the corresponding section title in
# a configuration file, e.g.
#
# [setup]
# channel width = 20
# chip region = channel
# ...
# [i... | ZELLMECHANIK-DRESDEN/rtdc_hdf5 | Python/meta.py | Python | bsd-3-clause | 5,818 | [
"Gaussian"
] | c155fbfaab14234f8b9850c9db6aa0896e2642612a2381701128a2418616e3db |
# Copyright 2012, 2013 by the Micromagnum authors.
#
# This file is part of MicroMagnum.
#
# MicroMagnum is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) a... | MicroMagnum/MicroMagnum | src/magnum/micromagnetics/io/write_vtk.py | Python | gpl-3.0 | 1,978 | [
"VTK"
] | 000a0f1c3bfee6062ebe1a4dfe3961e73e0d8c3f9446eeb11bef3acf842346c9 |
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #
# (c) 2010... | liuwenf/moose | python/chigger/filters/__init__.py | Python | lgpl-2.1 | 1,914 | [
"MOOSE",
"VTK"
] | 144709923087a91aa761df76db18d6c327e19f1d2ca84bb95c7c4af83e239013 |
# -*- coding: utf-8 -*-
# Copyright (c) Vispy Development Team. All Rights Reserved.
# Distributed under the (new) BSD License. See LICENSE.txt for more info.
from __future__ import division
import numpy as np
from ..gloo import Texture2D, VertexBuffer
from ..color import get_colormap
from .shaders import Function, ... | Eric89GXL/vispy | vispy/visuals/image.py | Python | bsd-3-clause | 18,615 | [
"Gaussian"
] | 5c0b455d25edb3b8b295a1093fc2f5e6cb7ee61d9628dabbcf7c0bb62f224f45 |
"""
Maximum likelihood covariance estimator.
"""
# Author: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Gael Varoquaux <gael.varoquaux@normalesup.org>
# Virgile Fritsch <virgile.fritsch@inria.fr>
#
# License: BSD 3 clause
# avoid division truncation
from __future__ import division
import warnin... | Tong-Chen/scikit-learn | sklearn/covariance/empirical_covariance_.py | Python | bsd-3-clause | 9,099 | [
"Gaussian"
] | 5c13fe98f1b78b2a79a090d89c9e98e9f2d8691285c0d124fd858596afba84e4 |
# $Id$
#
# Copyright (C) 2000-2006 greg Landrum
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" Matrix operations which may or may not come ... | adalke/rdkit | rdkit/ML/MatOps.py | Python | bsd-3-clause | 805 | [
"RDKit"
] | de1bbeda4a94aeee3f3914e31fe19a855b7aad8fde2fe97193982eb06366ec1e |
"""Analyse the polarity of cells using tensors.
This script makes use of a Gaussian projection as a pre-processing step prior
to segmentation of the cell wall and marker channels.
"""
import os
import os.path
import argparse
import logging
import PIL
import numpy as np
import skimage.feature
from jicbioimage.core.u... | JIC-Image-Analysis/leaf-cell-polarisation-tensors | scripts/automated_gaussproj_analysis.py | Python | mit | 5,901 | [
"Gaussian"
] | 57f28755a387a80b1e0d1faf0f5ac14692d5dc3b74bc0a81c9a59fd520ffc765 |
#************************************************************************
#
# PathFinder: finding a series of labeled nodes within a
# two-layer directed, cyclic graph.
# Copyright (2013) Sandia Corporation
#
# Copyright (2013) Sandia Corporation. Under the terms of Contract
# DE-AC... | Mantevo/PathFinder | ref/graph_gen.py | Python | lgpl-3.0 | 10,752 | [
"Brian"
] | 83675ee1d81a046c219976a9ea959ede8686959411522282ce46802be6f316f0 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Tests for the bencode parser plugin for Transmission BitTorrent files."""
import unittest
from plaso.lib import definitions
from plaso.parsers import bencode_parser
from tests.parsers.bencode_plugins import test_lib
class TransmissionPluginTest(test_lib.BencodePlug... | kiddinn/plaso | tests/parsers/bencode_plugins/transmission.py | Python | apache-2.0 | 1,725 | [
"Brian"
] | e9f579cee466b1b66823e2e6af30a49af31c056007c570426ac7a0ae767487a6 |
"""
Regularized Regression Example
------------------------------
This performs regularized regression on a gaussian basis function model.
"""
# Author: Jake VanderPlas <vanderplas@astro.washington.edu>
# License: BSD
# The figure is an example from astroML: see http://astroML.github.com
import numpy as np
from matpl... | nhuntwalker/astroML | paper_figures/CIDU2012/fig_rbf_ridge_mu_z.py | Python | bsd-2-clause | 3,158 | [
"Gaussian"
] | e0159de826c10d0b7c5b66e0dacc67c6ffd777cfbc68d653bc9158a50e1d5019 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
Created on Jul 30, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "Jul 30, 2012"
import unittest
impo... | Dioptas/pymatgen | pymatgen/io/tests/test_smartio.py | Python | mit | 2,675 | [
"pymatgen"
] | 4573d4b8e636fc7c738ab47324d924a74c01dfe079306326b4e1cf7096c97486 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/cc/test/test_dfccsd.py | Python | apache-2.0 | 9,940 | [
"PySCF"
] | 484f12f9a7bd0ab39ead153a4fdd03e01e0677a20c2cbeb8af1598118db4d066 |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding model 'RawIncomingEmail'
db.create_table(u'mailit_rawincomingema... | TEDICpy/write-it | mailit/migrations/0004_auto__add_rawincomingemail.py | Python | gpl-3.0 | 11,701 | [
"VisIt"
] | 713167e4c8e932e448a97f3b602f014b80f305b5a80147ec22842c396b56c3c2 |
import time
import json
import cgi
import threading
import os.path
import re
import sys
import logging
import lesscpy
from six import StringIO
from http.server import BaseHTTPRequestHandler, HTTPServer
from socketserver import ThreadingMixIn
from http.cookies import SimpleCookie
from urllib.parse import unquote, quote... | philsitumorang/thorin | thorin/server.py | Python | mit | 19,933 | [
"GULP"
] | 8056ff271ccbc17f7babf739380c53791d01ae1cdd57bbd7b4b8d6b7320a069e |
#!/usr/bin/env python
############################################################
from vtk import *
############################################################
# Create pole for camera aim and polar axes pole
pole = [1., 12., 3.]
# Create camera
camera = vtkCamera()
camera.SetClippingRange( 1.0, 100.0 )
... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/LIC/Python/CylinderAndPolarAxes.py | Python | bsd-3-clause | 3,133 | [
"VTK"
] | dc3c43c6a0715c97ba65fb9ea03c36a718caeeb927c4a8993caa85c8362910fb |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2005 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Andrew I Baznikin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Ge... | pmghalvorsen/gramps_branch | gramps/plugins/rel/rel_no.py | Python | gpl-2.0 | 9,799 | [
"Brian"
] | 1af2a0ffb80982bec274a81234d9b22f3f749f69118fdc77af584807f1100c85 |
import pysam
import pandas as pd
import collections
import copy
class granges:
def __init__(self, lengths = None):
# Read in chromosome lengths
if lengths.endswith('.fa') or lengths.endswith('.fasta'):
in_file = pysam.FastaFile(lengths)
self.lengths = collections.OrderedDic... | adam-rabinowitz/ngs_python | ranges/granges.py | Python | gpl-2.0 | 6,114 | [
"pysam"
] | d733c9720babde94299e9e5e91c776f0e0b5f32d3f11ec3b5d07dd8db602e4bc |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | le9i0nx/ansible | lib/ansible/modules/network/avi/avi_applicationpersistenceprofile.py | Python | gpl-3.0 | 7,203 | [
"VisIt"
] | 0acdfde783027229a7231eb99accef16ecf181af44a97f3cb25dff764465cbbb |
#!/usr/bin/python
"""Test of sayAll."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
#sequence.append(WaitForDocLoad())
sequence.append(PauseAction(5000))
sequence.append(KeyComboAction("<Shift>Tab"))
sequence.append(KeyComboAction("<Shift>Tab"))
sequence.append(KeyComboAction("<Control>H... | GNOME/orca | test/keystrokes/firefox/say_all_bugzilla_search.py | Python | lgpl-2.1 | 9,712 | [
"ORCA"
] | 2177a2bd0dc025eedab3d7a1ee15fb89099be613efad5641ea96f39b7abf442b |
# Copyright (C) 2001-2021 greg Landrum
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""basic unit testing code for the molecule boost wrapper... | greglandrum/rdkit | rdkit/Chem/UnitTestChem.py | Python | bsd-3-clause | 6,638 | [
"RDKit"
] | dfcb365a226d4833254ce95ec04fdf3be340b98cd4af9e0b7e9f51738421386a |
import os
from paraview.simple import OpenDataFile, RenameSource, Show
surfdir = "postProcessing/surfaces"
times = sorted(os.listdir(surfdir))
files = os.listdir(os.path.join(surfdir, times[0]))
for f in files:
file_list = [os.path.join(surfdir, t, f) for t in times]
OpenDataFile(file_list)
RenameSource... | petebachant/foamPy | scripts/pvloadsurf.py | Python | mit | 345 | [
"ParaView",
"VTK"
] | 89941a69ec955e56b871ecb844619f76c765376baab4d9301b05d029f13078d7 |
from __future__ import division
import tornado.ioloop
import tornado.web
import tornado.httputil
import tornado.gen
import tornado.escape
import numpy as np
import matplotlib
#matplotlib.use('Agg')
from matplotlib import pyplot as plt
from netCDF4 import Dataset
import datetime
import glob
import io
import os
import ... | davesproson/mappy | app.py | Python | gpl-3.0 | 13,410 | [
"NetCDF"
] | 9b2344e64a5241428710bd7e422b59bb81660cb558a8271e4067bc8296a0b7b5 |
import numpy
import mcfit
from scipy.interpolate import InterpolatedUnivariateSpline
from .power.zeldovich import ZeldovichPower
NUM_PTS = 1024
def xi_to_pk(r, xi, ell=0, extrap=False):
r"""
Return a callable function returning the power spectrum multipole of degree
:math:`\ell`, as computed from the Four... | nickhand/nbodykit | nbodykit/cosmology/correlation.py | Python | gpl-3.0 | 4,517 | [
"Gaussian"
] | 4639a13f4648e647c70291d067beb7f7963e8a206332b2e2bd0ff458519b8695 |
'''
Created on Feb 1, 2017
@author: Alexandre Day
Purpose:
Perform density clustering on gaussian mixture
'''
from fdc import FDC
from sklearn.datasets import make_blobs
from sklearn.preprocessing import StandardScaler
from sklearn.metrics import normalized_mutual_info_score as nmi
from fdc import plotti... | alexandreday/fast_density_clustering | example/example_test.py | Python | bsd-3-clause | 1,525 | [
"Gaussian"
] | e0e490451a923b97f329859323e39e67af50386ee85d3bfdab9601bfd684e967 |
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